The Atlantic cod (Gadus morhua) has a long history as a commercially important species in the North Atlantic and adjacent waters. The decline in the capture fishery has resulted in a shift towards the production of Atlantic cod using aquaculture in a number of countries, including Canada. Selective breeding is a proven, powerful approach in the enhancement of domesticated species for food production. In order to develop an efficient breeding program, it is desirable to generate suitable molecular tools in order to accelerate the selection process. The application of genetic tools in finfish aquaculture breeding programs has only recently become standard practice (De-Santis and Jerry, 2007). Currently, 10 out of 19 major aquaculture species are being produced using selective breeding for improved broodstock selection and new tools are being developed to make selection more precise with the ability to identify and locate quantitative trait loci and then use markers assisted selection to speed the selection process (Hershberger, 2006).
Accordingly, a dense linkage map linked to traits of economic importance would represent one of the most useful genomic tools for application in the selective breeding of Atlantic cod. A variety of different marker types such as amplified fragment length polymorphisms (AFLPs), microsatellite markers or SNP markers can be used for linkage mapping or association mapping. SNPs have become a focus of marker development in many species in recent years due to their abundance and low cost of genotyping allowing the construction of a high density map. In aquaculture species, SNPs are especially important if they cause differences in economic traits or are linked to such a trait. SNPs developed from collections of expressed sequence tags (ESTs) can be particularly valuable as they can be used to identify changes in the amino acid sequence of encoded proteins, also known as non-synonymous SNPs (Kim et al., 2003).
The increased number of ESTs available for fish has facilitated the detection of SNPs for different fish species. Significant numbers of SNPs have been reported in channel catfish (He et al., 2003), salmon (Hayes et al., 2007; Smith et al., 2005) and sea bream (Cenadelli et al., 2007).
With respect to Atlantic cod, Moen et al. (2008) recently developed a large number of SNPs from ESTs based on 5′ sequence reads. One SNP has also been identified for the pantophysin (Pan I) locus (Delghandi et al., 2007)
There remains a need for high quality SNP markers and SNP markers associated with traits of commercial importance suitable for the genetic analysis of Atlantic cod.